Into the Storm
by littleREAofsunshine
Summary: When Clint Barton ends up on a SHIELD base during the HYDRA invasion, he knows he needs to find a way out (preferably alive) so that he can warn Nat and Steve. Having to blend in with the Agents around him, he isn't sure how far he is willing to go to keep his cover, or who he will have to betray. Basically, takes place during CAWS and has Clint Whump/ Hurt Clint/Clint Torture YAY
1. Chapter 1

**A/N**

**Hello! Welcome to my story! I am so glad you guys decided to take a peek at my story I've got going on here. Just a couple of things you should know, my Clint Barton was 29 during the events of Loki's invasion, so he is pretty young. My Natasha Romanoff has the Russian version of the super soldier serum and is older than she appears. In this story, Clint Barton does not have a family. Also I need Title ideas. I just put this because it sounded dramatic.**

**Now that you know all that, let's move on to the story.**

**Disclaimer: Although I want this to be a claimer, I own nothing MARVEL except for a few figurines.**

**Also, Please read the Author's not at the end. This isn't much, but I need ideas (explained in Author's not at the end) before I get further, everything else has been mapped out except for this one thing. ****Read and Review! **

As Clint snuck out of the infirmary, he knew something was wrong. Yes, he hadn't told anyone he was leaving -they couldn't make him stay- but usually, someone found out he had left pretty quickly. Normally either Phil or Natasha was there too and since Natasha was on a Mission with Steve and Phil was - well, there was no reason for anyone to come looking for him and the nurse knew he did this a lot.

Taking it for the infirmary nurses being used to the treatment and 'jail' breaks, he made his way back to his room, he felt naked without his gear. He was always in defense mode, always ready to fight, it was ingrained into his DNA, he would always fight back.

As he rounded the corner of the hallway with his room, he heard guns being fired. He entered his room as fast as he could and watched through the door as heavily armed troops ravaged their way through the residence area, shooting to kill anyone who got in their way.

He held his breath as they approached a young agent, Mills if he recalled correctly. He recognized Mills, he had been in his trainee group a year or so ago, and was one of the newer agents. He didn't want to watch as the kid got slaughtered, but he knew he wouldn't be much use to SHIELD if he was dead.

He watched, quickly changing and arming himself - can't protect the base in hospital garbs - and was shocked when what was clearly the team leader stopped, not shooting Mills. He only realized the severity of the situation when he heard two words come out of the present agents', including Mills's, mouths:

"HAIL HYDRA"

**A/N**

**OHHHHH Exciting. Okay, so I have the entire story mapped out except for this one part. I need you guys to give me ideas of ways HYRDA should 'test' Clint to see if he is really on their side. Please PLease PLEASE Comment your ideas and Review. I need constant love (and constructive criticism)**

**Catch ya on the Flip side**

**littleREAofsunshine**


	2. Chapter 2

**A/N**

**Welcome back!**

**So, this is probably the fastest I****have ever updated. I really need ideas guys so either comment or PM me with your ideas.**

**Disclaimer: I own nothing except a couple FunkoPops and the story**

**Read and Review! **

_Last time:_

_He watched, quickly changing and arming himself - can't protect the base in hospital garbs - and was shocked when what was clearly the team leader stopped, not shooting Mills. He only realized the severity of the situation when he heard two words come out of the present agents', including Mills's, mouths:_

_"__HAIL HYDRA"_

Clint paled as he realized the disaster he had gotten himself stuck in. SHIELD was being taken over by HYDRA. HYDRA was SHIELD, and he just _had_ to be on base when it happened - great just great- he just needed to find a way to make it out, preferably alive. Once he dealt with himself he would find Tasha, hopefully, she didn't get caught in any trouble, but he knew their record, and since when had things ever gone their way.

Now in his black SHIELD gear (his Avengers uniform still in Stark Tower for repairs), armed with a couple of guns, his knives, and his quiver he was beginning to regret leaving is bow in the armoury. He would just have to grab it on the way out.

He watched as the troops left the hallway before sneaking into the hallway himself. He knew if he could get into the server room, he could save files and the erase the system, keeping HYDRA from getting their hands on SHIELD weapons, he just had to get there first.

He knew the New York base by heart. It was his home, it was where he used to feel safe. So when he heard the group of HYDRA agents come closer, he knew exactly how to get into the vents unseen.

Once in the vents, Clint knew how to maneuver to the Server Room. It was difficult, every move sent his quiver scraping across his back, that would leave a mark, but he managed to get to the vent cover that opened directly in front of the server room.

Checking to make sure the hallway was clear, he quietly dropped to the doorway. He held his breath as he used the palm scanner hoping he hadn't been taken out of the system, only breathing once the door was shut behind him.

He pulled out the flash drive he had grabbed from his gear - you never knew when a bad guy would have valuable information - and plugged it into the nearest computer, downloading as much as he could as quickly as possible.

He looked at his watch, cursing when he realized he had been there for two minutes. He had managed to download most of the information, but HYDRA would be there by the time he wiped the systems.

He glanced at the door, hiding the hard drive in his quiver - he'd thanked Coulson for being so smart and including a hidden compartment- before focusing back on the computer. He prepared to send a message, snapping around, having heard the door open.

Approaching him were about ten agents, headed by a man he knew was Caleb Ryder, he had done a couple of missions with him before.

He knew he had to make a decision. He could easily take down the ten men, but then he wouldn't be able to get any more information, everyone would know he was SHIELD. But if he played as HYDRA, sure he might get some information, but if he got caught, he wouldn't be able to do anything with it. He made his decision.

He needed to know what happened to Nat and Cap.

"Agent Barton," He heard Ryder call out, "What do you think you're doing?"

"I figured we might want to get a copy of all the files in case some decides to wipe the system"

"It's good to know you are with us"

"Hail Hydra" the words slipped easily off his tongue. This is what he did well, he could blend in, gain their trust, betray them later. It seemed he was good at betraying people

"We can get someone else to copy the files, I'm sure the boss will have a better use for you"

Clint only nodded, he wasn't particularly fond of being referred to as a tool, something to be used, a pawn, but the council liked to make it very clear that that was exactly what he was, a weapon, something to be used and then discarded. Although, Natasha would argue that good weapons were meant to be cherished.

He held back a snappy comment knowing it wasn't just him on the line this time. The faster he could find Nat, the better.

The trip to the hangar was quick and uneventful. He was horrified by the amount of bodies lining the corridors. These were coworkers, trainees and veterans alike, all lying dead at his feet.

That seemed to be a common theme recently.

HYDRA shouldn't have been able to take SHIELD so easily. He should have seen it coming, his job was to see things that others couldn't.

He could dwell on his failures for very long, he could see the hangar entrance ahead.

He used his remaining time to reinforce his defenses and cover. His defenses were always up, but he knew he couldn't let anyone as much as wonder if he was on their side. He needed their trust, and judging by the prisoner-like way he was being escorted, they didn't trust him. Not yet.

As he got to the hangar, he was shocked to see how many people he recognized. People he had worked with on a daily basis, just running around taking control of the base, like they were never loyal. Well, they never were, he thought.

Another man he recognized, Ian Michaels, seemed to be in charge of it all. Ian was older than him, late 30s at the youngest, but he had never really trusted him, something always seemed off with him. He had worked with Clint a couple of times when Coulson wasn't around, but other than that, he didn't really know him.

"Agent Barton," he said, "I wasn't expecting to see you here"

"Well I would hope so, if you did then I wasn't doing my job very well"

They both stared at each other. He could tell Michaels didn't trust him, not at all, he was going to have to prove himself to him.

"I guess there's a reason they say you're the best," he said, maintaining eye contact, "Your _skills_ will be very useful to the cause"

"I'm glad I could be of help," Clint decided to push his luck, "But I'm not much use without my bow. Do you mind if I go to the armory to grab it"

"I'll have someone grab it for you",

Well, he tried. "Thank you, Sir"

Hamilton Collins was the lucky tech who had been in the server rooms when he heard the alarm go off. Although he wasn't proud to say it, he hid. He couldn't hack anything if he was dead now could he.

He wasn't sure how long had passed before he saw Agent Barton enter the room. He had never actually met BArton, he had just heard about him. Before the invasion of New York, he had heard people describing him as a legend, one of if not the youngest SHIELD recruit in history. He had heard a couple jealous comments as well. People did understand how someone so young could be Fury's most trusted agent, everyone knew it was true. But after New York, the comments changed. It was no longer jealousy or awe, it was hate or pity. People didn't understand how Fury still trusted him, how he was still an agent. Collins wasn't sure how he felt.

He watched with a careful eye as Barton began messing with one of the computers, copying something. Was he going to wipe the drive?

Collins felt like an idiot, the first thing he should have done was copy the files and wipe the system, it would send out an alarm to SHIELD bases all over the world and protect the information.

He stifled a gasp as the door slammed open and a group of men entered.

"Agent Barton," the clear boss shouted "What do you think you're doing?"

"I figured we might want to get a copy of all the files in case some decides to wipe the system"

Why was a SHIELD agent worried about the information being deleted?

"It's good to know you are with us"

With who?

"Hail Hydra"

Collins couldn't believe his ears. It was worse than he imagined, HYDRA was in a SHIELD base, and Barton was with them. But Barton was loyal to SHIELD, right? If HYDRA had Barton, there was nope hope for leftover SHIELD agents in the base.

He didn't know what to do. Should he run? There was no chance of him lying, he was a horrible liar. Maybe he could alert another base.

He ran over to the now empty computer and saw that a message had already been prepared to send:

HYDRA HAS NEW YORK BASE. WATCH OUT

Praying the message was to someone he could trust, he replaced the message and hit send.

BARTON IS WITH HYDRA. NEW YORK BASE COMPROMISED.

He stood up, turned around, and prepared to find a way out. He was on the ground before he realized he wasn't alone.

Natasha Romanov looked at the message on her phone with a calm facade.

"Steve, we better get going, we've got work to do"

**A/N **

**That felt like it took ages to write, but it really isn't that long *sighs***

**This is actually all I have written for now. I NEED IDEAS PEOPLE. Seriously. Please give me ways HYDRA can test Clint's loyalty. Remember to leave a review, they give me motivation to write. **


	3. Chapter 3

**A/N**

**HEllo again, it has been a while. So update, I got busy. I'm not going to go into details, but life did it's thing and was a asshole. But I'm back and plan on writing a little more consistantly. This doesn't really mean much to you guys because it could be me sitting at my computer for 30 minutes and getting nothing done, or me sitting at my computer for 30 minutes and writing 5 pages, who knows. As always please read, review, comment, PM whatever you do becuase it keep sme motivated. If you have any suggestions leave them in the reviews. Have in constructive criticism: leave it in a review. Until next time.**

Natasha Romanov looked at the message on her phone with a calm facade.

"Steve, we better get going, we've got work to do" _

"What's up?" Steve shouted from the bathroom

"I just got a message on my phone from the New York SHIELD base, you should come look at this"

Steve looked at the message on the screen. He wasn't sure what to think.

BARTON IS WITH HYDRA. NEW YORK BASE COMPROMISED

He looked at the message, then at NAtasha and then back at the message,

"Do we believe it?" he asked hesitantly

"No" she snapped, "why would we believe it, he's Clint"

Steve felt horrible, but he still had trouble trusting Barton. He didn't know him like Natasha did. Clint seemed _dangerous_ so to speak. Yes, he realised that they were assassins, but Natasha made an effort to interact, to seem friendly, Barton didn't make that same effort. He was always on mission or hidden away somewhere. Steve was happy that they had convinced him to move into the tower, that didn't mean he fully trusted him. He trusted him, but not quite fully.

He watched as Natasha fiddled with the necklace around her neck. It was an arrow. Oh. He hadn't realized they were that close, he'd have to ask about it later.

"You'll just have to trust me with this" she looked him in the eye, "You don't know him like I do, but he …. " she sighed, contemplating what to say,"He wouldn't betray us"

"Okay then, let's take SHIELD back"

Clint had been following Michaels around for quite some time when the trainee came back with his bow

"Here you go,Sir" he seemed hesitant, they still didn't trust him.

"Thanks"

He walked back to Michaels who had wandered off during his short interaction with agent and appeared to be speaking with the head of a different strike team.

"Sir, we've almost got a lock on Director Fury's location." the agent reported, "Do want us to send the Soldier after him once we are sure?"

"That's _former_ Director, and yes, we need to take him out of the picture as soon as possible. Even with one eye he is a pain in my side"

Clint hesitated before approaching. They were trying to kill Fury. It wasn't going to be easy, but if they took Fury out, SHIELD was doomed. Steve was great and all, but he was no director.

"Agent Barton," Michaels shouted, "We've been doing some interrogations and found that one of the agents has been particularly troublesome and has outlived their use. We will be getting rid of him tomorrow, I expect you to be there to ensure no one escapes"

"Yes, Sir" he wondered, why would he need to go to an execution. Who was sentenced to die?

Clint entered the 'execution' room hesitantly. It was really just one of the interrogation rooms that wasn't being used. Like one of those cops shows, but instead of a table there was a dentist chair. They were going to use lethal injection. It was inefficient and a waste of resources, why would they do that.

Then it hit him. This was a test. _He_ was being tested. They wanted to see how he would react.

He took in a harp breath of air as he saw the man being led into the room. Jonah Richardson.

They had known each other for years, he had already been at SHIELD when Clint joined. He had been at this man's wedding. He was the closest thing he had to a friend before he met Phil and Nat.

Yet here he was, beaten and bruised, barely able to stand but with a fire still in his eyes. He held his head up and it highlighted the bruises around his eyes and neck. The cuts that littered his face. Clint wanted nothing more than to grab him and run, but he had to stay in character.

Clint watched hurt fall upon the man's eyes as he recognized him. The man looked as if he had suddenly given up, as if all fight had left him.

"You know," Michaels stated from the hallway, "He kept saying 'as long as the hawk lives, SHIELD has hope'", the man laughed, "this should be a fun surprise for him"

"You ready?"

"Let's get started"

He said something into a com device, but Clint wasn't paying attention. He was watching Jonah's face. The nurse preparing his skin for the injection.

He wanted to run in there in tell him not to give up hope. SHIELD would stay alive as long as he did. HE wanted to be there for the man who had been there for him, but he couldn't.

He looked up to see Micheals watching him, studying him. Jonah was dead no matter what he did. He couldn't blow his cover. At least, that's what he told himself.

He watched as the needle entered his skin.

He watched as his friend began to shake.

He watched as the man's body gave up.

He watched as his friend died.

Another person he could add to the list of people he couldn't save.

"Well, that was uneventful" Michaels sounded bored, like he had watched a bad movie

Clint just nodded.

"I'll meet you back in the conference room in two hours, you've got a mission"

Michaels entered the conference room early to be immediately questioned by a lower ranking officer.

"Sir, with all due respect, are you sure this is a good idea"

"Are you questioning my judgement, Agent Cassius?"

"No, sir. I'm questioning Barton's motives," he paused, gauging his superior's reaction, "Sir, Agent Barton has never shown anything but loyalty to SHIELD, why would he suddenly be working with us. I just don't think we can trust him"

Michaels sighed, he had had the same thoughts, "Cassius, he passed our tests, if the heads say to send him after Rogers, then we send him after Rogers. But if he tries anything, we'll know"

He looked at the time, annoyed, "He should be here any , be assured, we _will_ know if he tries _anything_".

Clint walked towards the conference room, fully armed in his black SHIELD gear, bow and quiver on his back.

To say he was worried would be an understatement; he hadn't expected them to send him on a mission this early. He was grateful, it would give him a chance to find Natasha and Rogers. He was worried he would be sent after Fury.

It was common knowledge amongst their little group (Romanoff, Hill, Coulson, Fury, and himself) that Clint could easily take down Fury if needed. There was no excuse for him if he let Fury get away. Hopefully, if he was sent after Fury, the agents didn't know that.

He hoped they sent him after Rogers or Natasha, they might know where the other one is, and they are the only two people who had a chance at taking him down.

Walking into the conference room, he was greeted by 5 pairs of cold eyes. Michaels, two older men, and a couple of younger agents who looked like they didn't really have a reason to be there.

"Agent Barton, please take a seat"

He looked over to see Michaels looking at him with waiting eyes. He wondered what he was waiting for. He opted to take the safe route and just sat down. He looked at one of the younger agents and was surprised to see they looked worried. Generally when meeting new or younger agents, he was met with awe, disbelief, and the occasional egotistical agent who thought they were better. Recently it was fear, but he didn't blame them. Who wouldn't fear him after the events of New York. Clearly, this Agent wasn't comfortable with the idea of sending him on a mission. His thoughts were disrupted by one of the older men clearing his throat, probably to get his attention.

"Now that you are here, let's get down to business. Agent Cassius?"

"Yes, Sir." The Agent he had been watching earlier moved to the front of the room.

"We have gotten a confirmation on the Location of Agent Rogers in the DC area. We assume he is working alone since there have been no other sightings in the area, but this is the first confirmation we have gotten since word of SHIELD's fall got out. We have a helicopter ready to take Agent Barton to the city, alone. He will be equipped with standard communications gear and will have access to the safe house in the city center as well as two options for a rendezvous point."

He looked at Clint before continuing, "Agent Barton, you will have to locate Rogers and confirm his location with the base before making a move"

"And Barton," the older man cut in, "your job is to locate and bring in Rogers using any means necessary. Alive or dead, bring him in. I know he used to be his teammate, but assume you can deal with it"

"Sir," he paused, "I am as close to Rogers as a cat is to water"

The older man chuckled, "I was wondering when we'd get to see that famous mouth of yours at work"

"When do I depart, Sir?"

"Tonight. Settle in, tell us if you need anything, and begin your task in the morning", he began to walk to the door, "dismissed"

He hurried out and headed back to his room. He needed a plan.

_  
**A/N**

**Sooooooo... there was that. It's not my best nor my longest work, but it has been a while so here you guys go. Please please please please comment/ review. Seeing reviews keep me motivated to write more. **

**If you have any suggestions leave them in the reviews. Have****in constructive criticism: leave it in a review. Until next time.**


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